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<h1 align=center>MarvinSpace Application Options</h1>
<h3 align=center>Version 5.3.1</h3>

<p>MarvinSpace is a 3D molecular visualizer application to display
macromolecules like proteins, protein-ligand complexes, RNA/DNA.<br>
It is available as part of the Marvin Beans package.
</P>

<h2>Usage</h2>

<blockquote>
<font COLOR="#333399"><strong>mspace</strong></font> [<em>options</em>] [<em>structure files</em>]
</blockquote>

<p>
<h3>Options</h3>
<table CELLSPACING=0 CELLPADDING=4 BORDER="0" class="grid" width="70%">
<tr><td><code>-h</code>, <code>--help</code></td>
    <td>
	print command line help
	</td></tr>
<tr><td><code>-</code></td>
    <td>
	import structures from standard input	
	</td></tr>
<tr><td><code>-v, --verbose</code></td><td>verbose mode</td></tr>
<tr><td><code>-c, --columns &lt;number&gt;</code></td>
    <td>
	the number of visible columns (maximum: 5)
	</td></tr>
<tr><td><code>-r, --rows &lt;number&gt;</code></td>
    <td>
	the number of visible rows (maximum: 4)
	</td></tr>
<tr><td><code>-n, --nMols &lt;number&gt;</code></td>
    <td>
	the number of molecules to import (default: 1000)
	</td></tr>
<tr><td><code>--multiCell &lt;number&gt;</code></td>
    <td>
    loads every input molecule to an empty cell
    </td></tr>
<tr><td><code>--singleCell &lt;number&gt;</code></td>
    <td>
    loads every input molecule to the same cell
    </td></tr>
<tr><td><code>-q, --quality ( L[ow], M[ed], H[igh] ) (default: Med) </code></td>
    <td>
	sets display quality
	</td></tr>
<tr><td><code>-p &lt;string&gt; &lt;string&gt;</code></td>
    <td>
    display property
    </td></tr>

</table>

<p>Multiple structure files can be passed in the command line. However,
the number of molecules actually displayed is influenced by other parameters,
namely <code>-n</code>, <code>-c</code> and <code>-r</code>. The number of cells
(and thus the number of structures displayed) is the minimum of the product
of row count and column count and the number of structures specified
by the <code>-n</code> option. <!--When <code>-n</code> is given without specifying
the number of rows and cells all input structures are displayed in the same cell.-->
<br>
Note, that the maximum number of cells is limited to 20.
</p>

<p>Note, that <a href="javaoptions.html">Java VM options</a> (like heap size)
can be passed to JVM through the mspace command line.</p>

<h2>Examples</h2>

<ol>
<li>Display the macromolecule defined in the given PDB file:
     <pre>mspace 4DFR.pdb</pre>
<li>View the first 6 structures from the given input file in a 2 rows by 3 columns table :
     <pre>mspace -r 2 -c 3 molecules.sdf</pre>
<li>View upto 10 structures defined in an SDFile in the same cell:
     <pre>mspace -n 10 --singleCell ligands.sdf </pre>
<li>Show the macromolecule defined in the given PDB file with the highest
display quality :
     <pre>mspace -q High 1AID.pdb</pre>
<li>To display verylarge structures the heap size should be increased, in particular
for surface calculations.
     <pre>mspace -Xmx256M 1FFK.pdb</pre></li>
</ol>

<p>MarvinSpace <a href="../developer/space-par.html">Parameters and Events</a></p>
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